Search and Analysis of Enzyme Data

The initial rate enzyme kinetics uses very low enzyme concentrations (e.g., 0.1 juM to 0.1 pM) to investigate the steady-state region of enzyme-catalyzed reactions. To investigate an enzymatic reaction before the steady state (i.e., transient state), special techniques known as transient kinetics (Eigen and Hammes, 1963) are employed. The student should consult chapters of kinetic texts (Hammes, 1982 Robert, 1977) on the topics. KinTekSim (http //www.kintek-corp.com/kintek-sim.htm) is the Windows version of KINSIM/FITSIM (Frieden, 1993) which analyzes and simulate enzyme-catalyzed reactions. 

SEARCH AND ANALYSIS OF ENZYME DATA 7.3.1. Search for Enzyme Database 

LIGAND (Goto et al., 2002) at http //www.gebine.ad.jp/dbget/ligand.html is a composite database comprising 

Note K u and K -,e or Kles and K2cs are ionizing groupfs) in the free enzyme or the enzyme-substrate complex, respectively. 

Cloned, pH stability, Temperature stability [°C], Organic solvent stability, Oxidation stability, General stability, Storage stability, Renatured, and Links to other databases and references. 

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Enzymes are biocatalysts, as such they facilitate rates of biochemical reactions. Some of the important characteristics of enzymes are summarized. Enzyme kinetics is a detailed stepwise study of enzyme catalysis as affected by enzyme concentration, substrate concentrations, and environmental factors such as temperature, pH, and so on. Two general approaches to treat initial rate enzyme kinetics, quasi-equilibrium and steady-state, are discussed. Cleland s nomenclature is presented. Computer search for enzyme data via the Internet and analysis of kinetic data with Leonora are described. 

Increase in sensitivity and efficiency of analysis in structural studies of enzymes with a gas phase sequencer have made it possible to determine the primary structure in a shorter period of time with a small amount of enzyme at the picomole or even femtomole level. In addition, thanks to the DNA sequencing technique the number of enzymes (or proteins) whose amino acid sequences are registered in a data base file has expanded explosively. The introduction of mass spectrometry on the primary structure determination of protein has stimulated the search for a new methodology other than Edman chemistry. 

MOE assigns a value of 1 or -1 for chiral molecules and zero for achiral molecules. DAPPER, was developed with this in mind and therefore can easily incorporate different conformation search techniques and chirahty metrics. A new chirality measure provides a quantitative description of the overaU chirahty of a given conformation of a molecule without assigning values to individual atoms. In this article, they discuss the analysis of several implementations of various conformation search techniques, a novel chirahty metric, and their incorporation into DAPPER with validation on three standard medicinal chemistry data sets (dihydrofolate reductase, angiotensin converting enzyme, acetylchohn-esterase). They have demonstrated clear predictive power in the case of 20 DHFR inhibitors [48]. 

The 631 nucleotide region, on analysis, showed restriction sites for a large number of restriction enzymes like Kpnl, SauSA, Smal, Xbal, Xmal, Sail (one site each), etc. The sequence had higher GC content, with 28.0% C and 29.3% G residues, than AT content the percentages of A and "F were 23.3 and 19.4, respectively. It codes for a polypeptide of about 21 kD. However, the nature of the protein and the mechanism of degradation of BOAA is not understood. Homology search did not reveal any homology with any of the known bacterial decarboxylase or deaminase which are present in our data base. 

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